These data are pertinent to our forthcoming publication in Cell Reports. These are the raw data files from Nanostring analysis of RNA extracted from F6 cells exposed to BMP4+FGF2 for 72 hours, then EGF+FGF2 +/- doxycycline and/or chiron for 48 hours. Samples labelled BG were exposed to EGF+FGF2 alone, samples labelled D were exposed to EGF+FGF2+Dox, samples labelled C were exposed to EGF+FGF2+Chiron, samples labelled DC were exposed to EGF+FGF2+Dox+Chiron. RNA was extracted from cells, and gDNA eliminated, using the RNeasy Mini Kit (Qiagen, 74104). The Nanostring PanCancer Pathways panel was used. Hybridization, purification and imaging on the nCounter system were conducted in accordance with manufacturers’ protocols. Triplicate samples were analysed for each condition. These are the raw data files. For anaysis, raw protein count data were processed by applying background thresholding and content normalization in NanoString nSolver 4.0. Comparisons were made, by group, to the EGF+FGF2 alone condition.